From 50ff5b4581f20d296748bd3cf579613f822f4d2d Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 17 Jan 2013 00:28:36 +0000 Subject: [PATCH] inprogress --- forester/ruby/evoruby/exe/select_same_gn.rb | 6 ++++-- .../evoruby/files/test/select_same_gn_test.fasta | 18 +++++++++--------- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/forester/ruby/evoruby/exe/select_same_gn.rb b/forester/ruby/evoruby/exe/select_same_gn.rb index 66d3540..de61eed 100755 --- a/forester/ruby/evoruby/exe/select_same_gn.rb +++ b/forester/ruby/evoruby/exe/select_same_gn.rb @@ -53,6 +53,7 @@ module Evoruby next end + species = nil if species_re.match( name ) s_match = species_re.match( name ) species = s_match[1] @@ -70,7 +71,8 @@ module Evoruby all_seqs << mol_seq end else - puts "no species for: " + name + puts "error: no species for: " + name + exit end gn_match = gn_re.match( name ) @@ -88,7 +90,7 @@ module Evoruby gn =nil if gn_match - gn = gn_match[1] + gn = gn_match[1] + "_" + species else if IGNORE_SEQS_LACKING_GN puts "cannot be" diff --git a/forester/ruby/evoruby/files/test/select_same_gn_test.fasta b/forester/ruby/evoruby/files/test/select_same_gn_test.fasta index e42b0ff..1ef4efe 100644 --- a/forester/ruby/evoruby/files/test/select_same_gn_test.fasta +++ b/forester/ruby/evoruby/files/test/select_same_gn_test.fasta @@ -1,18 +1,18 @@ >a GN=nmi [XENTR] MDTSM ->d GN=akap17a [XENTR] +>b GN=akap17a [XENTR] MDT ->e [XENTR] +>c [XENTR] MDTSMEM ->b GN=nmi [XENTR] +>d GN=nmi [XENTR] MDTSMEMSRNP ->c GN=nmi [XENTR] +>e GN=nmi [XENTR] MDTSSEM ->f isoform [XENTR] +>f GN=nmi [DROME] +MDTS +>g isoform [XENTR] MDTSSEM ->f isoform [XENLA] +>h isoform [DROME] MDTSSEM ->f2 isoform 2 [XENTR] -MDTSSEM ->who are you +>h isoform [XENTR] MDTSSEM -- 1.7.10.2